conduitR

Overview

conduitR is an R package that provides tools for metaproteomics analysis using conduit and conduit-GUI. It offers a comprehensive suite of functions for processing, analyzing, and visualizing metaproteomics data. These functions are designed to be used in conjunction with the conduit and conduit-GUI packages, or independently for custom analyses.

Features

Getting Data

• Download FASTA files from UniProt and NCBI
• Download and process taxonomy data from NCBI
• Manage and combine multiple proteome databases

Data Processing

• Create custom protein sequence databases
• Associate sample proteomics data and metadata using QFeatures integration
• Transformation, imputation, and normalization of proteomics data
• Quality control and filtering options

Statistical Analysis

• Perform LIMMA differential expression analysis
• Support for various machine learning models:
  • LASSO regression
  • Random Forest
  • XGBoost
• Feature importance analysis and selection
• Statistical testing and multiple testing correction

Visualization

• Interactive heatmaps with customizable annotations
• PCA biplots with flexible aesthetics
• Taxonomic visualizations:
  • Barplots for abundance analysis
  • Heat trees for hierarchical relationships
• Volcano plots for differential expression
• KEGG pathway visualization
• Feature-specific plots
• Custom plot aesthetics and themes

Miscellaneous

• Comprehensive logging functions
• Error handling and validation
• Integration with existing bioinformatics workflows

Dependencies

The package requires the following R packages: - QFeatures for proteomics data management - limma for statistical analysis - ggplot2 for visualization - tidyr and dplyr for data manipulation - Additional packages for specific functionalities (see DESCRIPTION file)

Installation

You can install the development version of conduitR from GitHub:

r, eval = FALSE # install.packages("devtools") devtools::install_github("baynec2/conduitR")

Usage

This is a work in progress. The package documentation and vignettes will be updated with detailed examples demonstrating: - Data import and preprocessing - Statistical analysis workflows - Visualization techniques - Integration with conduit and conduit-GUI - Best practices and recommendations

Stay tuned for updates!